Children of the Atom
by hannibal1996
Summary: The MCU but with the addition of mutants who have existed the entire time but are trying to stay out of the superhero scene but when a Hydra prisoner escapes, the X-men and Avengers must unite together to stop the prisoner and a more dangerous opponent.
1. Chapter 1

**The Atomic age part 1**

 **Triskelion-1987**

Peggy Carter, director of SHIELD was walking down the corridors of the new headquarters, they hadn't finished building it yet but it was being used. She walked down a flight of stairs and into the basement of the facility where they had built a small prison. She opened the door and walked into the cell block, ten small cells all next to each other. In the middle of the room was a man in his mid thirties, sat in a wheelchair. He was staring at one of the cells, inside it was two guards and a masked prisoner.

"Charles Xavier, apologies for keeping you waiting." Peggy Carter said as she walked up to Charles Xavier, they shook hands and looked around the room.

"Don't worry about it my dear, gave me a few moments to reflect." Charles said as he looked at the cell.

"I'm sorry Charles but it's the best course of action." Peggy said. She looked at the cell and closed her eyes and started to think.

"I know...It's just, he is my friend after all." Charles said as he looked at Peggy.

"Friend or not...He's a killer." Peggy replied, Charles looked at her and smiled, he could feel something in her mind.

The guards walked out of the cell, pulling out their guns and pointing them at the prisoner as they shut the door. Inside was a man, around the same age as Charles but he was a tall, muscular man. He had light blonde hair

"Tell me Charles, do you ever wake up in the middle of the night? Afraid that they'll come to your school and take your precious children?" Erik said to Charles as he was getting prepped to enter the cell.

"I feel sorry for the fool who comes to my school looking for a fight." Charles replied. The two weren't looking at each other yet, they could barely look at each other.

"You can't build a prison to stop me Charles." Erik replied.

"Forgive me Erik." Charles begged.

"Forgiveness is for the damned." Erik said as he turned around, looking Charles right in the eye before entering the cell.

 **1991**

Erik was sat in his cell. He had been there for years, he had been there for so long he had lost track of time. He hadn't seen anyone for a long time, he had forgotten what people looked like. Then it happened, the door opened. He jumped up, ready to fight but he was greeted by a middle aged man in a suit...Alexander Pierce.

"Erik Lensherr...It's good to meet you." Alexander said as a group of men walked into the room and held Erik down. They had no metal on them and injected him with several chemicals.

 **2014**

Hydra have been exposed to the world after their plans were foiled by Captain America. SHIELD headquarters was destroyed by a helicarrier and along with the headquarters, the prison was as well.

Two guards were sprinting down the corridor to the prison as the ceiling started to come down, the place was in flames. The guard ran up to one of the cells and opened it, it took a moment for it to open but as it did the guard was hit by a gust of air. As he stepped back, a tall figure emerged from the cell. He hadn't aged since he was put in there, his blonde hair was still combed back and he was as angry as ever.

"Hail Hydra." The guard said, clearly nervous. The man looked at him and opened his palm, the guard looked at him for a second, even more confused now. A piece of metal flew into the palm of his hand and into the guard's throat.

"Never." The man said as he walked away.

 **2016-Westchester**

"Welcome to Charles Xaviers school for gifted youngsters, this as you know is a highly exclusive school and we only take very select students. To decide whether a student is eligible to join or not they will have to do our personality test." Ororo Munroe explained. She was the deputy principal at the school and was showing a family around the old house.

"I thought this school was open to everyone?" The father asked. He was dressed in a suit that looked like it had come from a charity shop, infact they all did.

"It is to everyone who meets our entry requirement." Ororo explained. She was an African woman who was wearing

"A curse?" The teenage girl asked.

"A gift." Ororo corrected.

"Hear that...A gift?" The mother said, trying to reassure her child. They were all to nervous.

Scott Summers, one of the students at the school was walking down the corridor. His sunglasses were hanging low and if you looked closely enough you could see a red tint in his eyes. His brown hair was like a mop today, he clearly woke up late. His jeans were baggy and he wore a random Captain america shirt that he found on the floor, he was practically running to his lesson.

"Ah Mr Summers, I see you finally made it." Hank McCoy said as Scott walked into the room. Hank or Beast as he sometimes called himself was at least seven foot tall and covered in blue hair. He looked more like a bear than a man but he always meant well.

"Sorry...I overslept." Scott said as he tried to slide into his seat.

"Well maybe you can tell me why the Weimar republic was always set to fail?" Hank asked. Scott was stood there, his face going red.

"Erm." He managed to slip out, Hank tried to hide his smirk but couldn't.

"Sit down Scott." Hank said. Scott then slid into his seat and tried to hide his face from the embarrassment.

Next to him was one of his oldest friends at the school, Rogue. She looked at him and couldn't help but smirk. She was a skinny girl, not particularly tall but she looked like she had been starving for a few days. She had a more gothic look to her than most of the students in the school, she had brown hair but a white streak in the middle of it and was wearing black leggings with a green shirt.

"Smooth." Rogue whispered under her breath.

 **X**

Jean was sat in Charles Xavier's office. She was trying to make a metal ball hover in the air, she was managing it but she found it rather difficult. She was one of the older students in the school and had been there longer than most.

"You're doing well Jean, very well infact." Charles said to his student. He was older than he once was, maybe to old to still be working in the school but he enjoyed it. He wore his blue suit that looked like it was freshly made just for that day, he was bald now and getting wrinkley, something he wasn't to happy about.

"I'm still struggling." Jean explained.

"Muscles have to be built, they have to be worked on Jean." Charles said, trying to reassure her.

"I know, its just….This is a stress ball, this is all I can manage." Jean explained as she picked it up.

"You'll get there Jean." Charles said.

"I know...Thanks professor." Jean replied. She was a little discouraged, she knew she would get there but it was going to take time.

"Anytime and Jean, if you have anymore nightmares do let me know." Charles said. Jean nodded and as got up to leave, David Haller walked in.

"Hey Jean." David said as Jean walked past him, trying to avoid any contact with him

"I don't think she's forgiven you David." Charles said as David sat down. He smiled and looked at his father.

"What can I say, the girl holds a grudge." David replied with his usual cocky attitude.

"You hurt her." Charles defended Jean, he knew what happened and it annoyed him that David didn't seem to care.

"It doesn't matter….Forgiveness is for the damned." David said with that smile again, that arrogant smile.

"You know I hate that saying." Charles said.

"Come on dad, it's just a saying." David replied but Charles just looked at him.

"You should be more careful David...Even today he still causes problems." Charles explained.

"You know he's dead right?" David asked sarcastically.

"I don't believe that even for a second….Now what was it you wanted?" Charles asked, he was beginning to get impatient.

"Cerebro." David said.

"You're not even close to being powerful enough yet." Charles replied bluntly.

"I am." David replied. He was getting frustrated, he had been trying to get to Cerebro for so long now but Charles had been refusing.

"It will hurt you David, you're not strong enough yet." Charles explained but it wasn't enough, David was to stubborn.

"Fine." David said, walking out of the room

 **X**

Logan, the Wolverine was sat in a bar outside of New York. He was drinking his fifth beer in the near empty bar, he knew the scent of everyone there and that's when it happened, he detected a new but familiar scent.

"Fury...It's been a long time." Logan said as he downed the last of his beer.

"I have news for you, some good news." The familiar scent said. Logan turned around to see it was Nick Fury and he was about to sit down.

"That's a first." Logan replied as he gestured for two beers.

"I've found Erik." Fury said as he threw a picture onto the bar. It showed Erik, still looking young at an airport in Sokovia.

"Where is he?" Logan asked as he looked at the picture. He knew it was him, there was no forgetting a man like Erik, even with Logan's memory.

"The motherland...He's on a quest to find his family." Fury said as he drunk his beer.

"Does he know?" Logan asked.

"I really hope not." Fury replied. Both men agreed, the last thing they wanted was an angry Erik.

 **X**

Erik was stood in the middle of a graveyard in Sokovia. He was stood over a grave that read 'Pietro Maximoff'. He fell to his knees as he looked at the grave, struggling to understand what had happened.

"I will take everything from them." Erik mumbled under his breath.

 **Well I hope you enjoyed so please review. This is just an experiment and I'll only continue it if you guys like it. Is there anything you want explained? What do you think Erik will do? This chapter focuses more on X-men but will be Avengers and X-men. What would you like to see? until next time, have fun.**


	2. Chapter 2

**Atomic Age part 2**

The Avengers, Earths Mightiest Heroes as they were often called, not everyone thought of them as heroes though, that's where everyone goes wrong. To some they are a militant group who march into countries and fight their own fights in another persons backgarden...To some the Avengers were villains, to some they needed to be stopped….This was the case for Erik Lensherr, the man out of time.

Erik was sat in a coffee shop in New York, he didn't really understand the world yet, he didn't know what was going on. He sipped at his coffee and looked at his hands, they were starting to shake a little. He was reading a newspaper about the superhero 'Civil War' and how some of them disappeared but he wasn't interested in the likes of Captain America or the Winter Soldier...He wanted the Scarlet Witch. He looked up at Stark Tower across the street and took another sip of his coffee.

"He normally shows up about now if that's what you're here for." The waitress said as she walked over to him.

"Thank you." Erik mumbled and she walked away. He looked at the tower and saw Iron Man fly towards it. He got up and left, walking across the street and straight into the building.

As he walked in, he couldn't help but think about Charles Xavier, he wondered where he was but at the same time didn't want to know. He stepped into the lobby and admired the heightened security but as he looked at the CCTV cameras they started to turn around. He walked towards the lift, using his powers to short circuit some of the wiring to cause a small explosion and attract the guards attention, allowing him to hold the lift and step inside. He forced the lift to go up and open at the floor Tony was on.

Tony was stood in the office, staring at Steves shield and trying not to breakdown. He missed Pepper, he missed Rhodey, he missed Bruce...He even missed JARVIS a little but as he got caught up in all of that he turned around to see Erik stood there, with that same expression.

"Uhhh...Who are you? Tourists aren't allowed in here." Tony asked as he walked over to Erik, making sure his watch was turned on.

"I'm looking for Wanda Maximoff...Where is she hiding?" Erik asked as he approached Tony.

"...What do you want with Wanda?" Tony asked. He stopped, his heart was beating as fast as it could and he saw the look on Erik's face.

"Where is she? Tell me." Erik said as he used his powers to make cables fall out of the ceiling and tie up Tony.

"FRIDAY...DO SOMETHING." Tony screamed out in horror as two suits activated and flew towards Erik but he caused them to fly into each other and then out of the window.

"Your metal suits are nothing against me." Erik yelled.

"Is that right." Tony said as Erik picked up the shield, admiring it like a child and then dropping it onto the floor.

"I've already let you take one of my children….Now where is my daughter?" Erik asked. Tonys heart stopped, he didn't know how to react to that.

"...Daughter?" Tony asked.

"TELL ME." Erik screamed as he forced a screwdriver to go into tony's side.

"I don't know...Steve took her somewhere...I don't know where." Tony screamed. He managed to press a button on his watch that sent out an alert.

"Mr Stark?" Vision said as he walked into the room, clearly alerted by the commotion. He looked at what was happening and immediately fired a laser to destroy the wires and free Tony.

Vision flew towards Erik but as he did, Erik threw the shield at him and then used his power to throw him into the ceiling. Tony jumped into a suit and fired at him but Erik used the shield to block it and then threw Tony into the floor and kept him there.

"Not getting this metal controlling thing are you….Now, where...Is..My...Daughter." Erik said as he tightened the metal, crushing Tony. He was also doing the same to Vision, trying to get information out of them.

"WAKANDA...She's in Wakanda...Dammit." Tony screamed. Vision looked at Tony, clearly upset and Erik walked out.

 **X**

Tony Stark was angry, he didn't know who this was or why he did what he did but all he knows is that he did it. He was sat in his office in the Raft, staring at Vision who just sat there. The Vision was clearly upset and Tony was angry, one of them needed to break the silence.

"How did you know?" Natasha asked as she watched the footage.

"They all went to Wakanda…" Vision replied. Tony knew and Natasha just looked at the two, a little angry.

"And her psychotic father isn't going to help either….Who is this guy?" Tony asked as he looked at the footage.

"I've been going through SHIELD files but so far I cannot detect anything." Vision replied.

"That's because SHIELD destroyed everything they had on him." Natasha replied.

"Go on then...Who is he?" Tony asked.

"His name is Erik Lensherr...He was a Sokovian freedom fighter during the eighties but was apprehended by SHIELD and taken into a secure facility and everything about him was destroyed….He was a legend in the Red Room, they say he killed some of the deadliest soldiers in the world." Natasha explained. She heard of Erik Lehnsherr or 'Magneto' as they called him.

"And how did he manage that?" Vision asked.

"Rumours were, were that he could control metal." Natasha explained.

"Great." Tony said as he leaned back in his chair.

"So where can we find him?" Vision asked.

"...I don't know but Fury might." Natasha replied.

 **X**

Charles was sat in his office with Logan and Fury. Natasha had contacted him about the incident in Stark tower and they had to call a meeting about Erik. Charles wasn't to happy that Erik was on the loose and didn't go to him about whatever Erik is after. Fury understood who Erik was and how dangerous he was whilst Logan just had a problem with him.

"So the incident at Stark Tower? How exactly did Vision become aware of Wanda's location?" Charles asked as he looked at the two grown men infront of him, depsite their reputations he was still acting like a headmaster.

"Vision is refusing to reveal that information but I'm pretty sure it has something to do with a Stark satellite and an untraceable mobile phone." Fury explained. Logan took out a cigar but put it back when Charles glared at him.

"She didn't get from you bub?" Logan asked.

"Now I never said that." Fury denied.

"We need to stop Erik getting to Wakanda, he could cause an international incident. We don't want a repeat of the Sokovian Civil War." Charles explained as he started to type on his computer.

"If we manage to arrest him, the UN will want you to come in as a consultant. Secretary Ross has already said your name several times." Fury explained.

"I thought you weren't with them anymore?" Logan asked. He was referring to SHIELD getting destroyed and Fury going into hiding.

"I'm not but I get curious." Fury replied.

"So what's the plan? Cerebro?" Logan asked.

"You know I would love to get my hands on that." Fury commented but as Charles started to wheel away he laughed.

"I'm sure you would Nicholas." Charles explained. Logan and Fury followed Charles towards Cerebro which was by the Danger Room.

The three entered the large room that was known as Cerebro. The room was dull and grey but it was filled with heavy machinery and a small table with a helmet attached to it. Charles wheeled up to it and put the helmet on, pressing several buttons which activated the blue lights and holograms on the table.

"Where are you Erik?" Charles asked himself as he pressed several buttons. Logan walked towards one of the computers surrounding the machine and started to press buttons on it, hoping to locate Erik.

Erik was in a hotel room, he was trying to work out how he was going to get into Wakanda to see Wanda and also investigating the death of Pietro at the hands of Ultron. He was staring at his board of suspects for Pietro and had a picture of Tony Stark in the middle of it, blaming him for his death.

"I had you Stark...I should have killed you when I had the chance." Erik said to himself, he was angry for not killing him then but he had to get out of there.

"Hello Erik." Charles said. He was sat in the corner of the room, talking to him through Cerebro.

"Charles..." Erik said in shock. He hadn't seen him in a long time, he was surprised by the way Charles looked, the whole world felt wrong to him.

"Erik what are you doing?" Charles asked.

"...My children are lost and buried Charles." Erik replied.

"You should have come to me, I could have helped you. They're coming for you now." Charles explained but Erik didn't care.

"That's what I want."

"To be arrested again?"

"They killed my son Charles...They put my daughter in a prison with a shock collar like an animal...I will take everything from them so let them come." Erik explained. Nobody knew about Wanda being locked up, it was classified information but Erik had his sources.

"Erik please, remember Sokovia." Charles begged.

"Charles...You were like a brother to me but you locked me in a prison...A prison where they did something to me." Erik said. He hadn't forgiven Charles for what had happened and he was still a little on edge

"Erik!" Charles screamed.

"My name is Magneto." Erik said as he revealed his helmet, Charles started to scream at him, begging him not to put it on but it wasn't enough. As soon as the helmet came on, he was Magneto and nothing could touch him. He pressed a button on his computer as the metal armoured plates started to fly towards him, he just revealed his location to the world.

"...We need to get him before they kill him." Charles said as he shut down Cerebro.

 **X**

Tony Stark was sat in his office, sitting and staring at a picture of Erik dressed as Magneto in the mid-eighties. Natasha walked in, clearly a little bit on edge but not as much as Tony.

"We've found him." Natasha said. Tony just stared at her until she walked out of the office and got out of his chair.

"Friday...Let's kick his ass." Tony said.

 **Well I hope you enjoyed so please review. How does Erik know about Wanda? What will Iron Man do? Until next time, have fun.**


	3. Chapter 3

Erik was sat in his hotel room. He knew what was coming for him and he was ready, he had several coins hovering in the air, circling him as he thought about his children. As he thought about Pietro and Wanda, he could feel the anger inside of him rise, knowing that they will never see him the same way they used to. Then it came, the sound of thrusters.

Erik looked out of the window to see Iron Man, Vision and War Machine flying towards him he smiled thinking how easy of a fight it will be. Why would they send three metal soldiers to fight the master of magnetism? As they got closer Erik thought about how he could escape but knew it would be a fight.

Iron Man fired a flash bang into the hotel, distracting Erik whilst Vision flew inside. Erik was trying to regain his sight whilst Vision approached him.

"It's over Erik, if you want to see Wanda again I recommend you come with us." Vision explained but Erik was not interested.

"My children went with you. One is lost and the other is buried...Why would I come with you." Erik hissed as he reached out his arm, controlling Vision. As he held him still, Vision unleashed a blast of energy from his gem, as it got closer to Erik something strange happened.

As the blast of energy got close to Erik, a flash of green light appeared and Erik had disappeared. Within the blink of an eye, Erik found himself in an old Sokovian church. He tried to work out what had happened but then he saw the green light moving around him.

"Who are you?" Erik yelled as the green light flickered around the church. Erik raised his hand, he could feel the metal in the blur, metal he can control.

Erik pulled the the green blur towards him, throwing it to the ground and holding it in place. The green blur eventually disappeared to reveal a young man, probably in his late teens or early twenties. He was wearing a green leather suit and had silver hair, he pulled off his goggles and wiped his eyes as he tried to get his breath back. Erik took a step back, stunned by how much he looked like his son, Pietro.

"Who are you?" Erik asked again but before he could get an answer, he was hit by a bolt of blue energy. He fell back but saw where it had come from and once again, he could feel the metal on their body. He brought the shooter forward to reveal another young man, probably the same age. The two looked similar the main difference was their hair, this ones was black like his daughter, Wanda. He had a black outfit with a red jacket.

"We remind you of anyone?" The black haired one asked. Erik started to get angry, is somebody exploiting his children to get to him? They will die for this.

"Grandfather, please...We need you to listen to us." The silver haired one asked.

"I'm Wiccan and he's Speed...We're you're grandchildren from the future and we need your help." Wiccan explained. Erik looked at them like they were insane but he thought he'd entertain them.

"From what?" Erik asked,

"Apocalypse." Speed replied.

"Incase you need help believing us." Wiccan said as he handed Erik a small envelope. He opened it to reveal a picture of himself with his children and the original brotherhood of Sokovia. Erik thought the photo had gone up in flames when the apartment was hit by a missile but here it was. Even if their story was a lie, they clearly wanted to work with him.

"If we're going to do this, we do it right….We need a new brotherhood." Erik replied.

 **X**

Ironman, Vision and War Machine were stood in the hotel room where Erik had been hiding. There was nothing helpful in the room, the blur had cleared it out. Tony was frustrated and the other two could tell. As they inspected the room, a small black place came heading towards them.

"Who are these guys?" Rhodey asked as he looked out of the window.

"Potential hostiles. I'll deal with them." Vision replied as he flew out of the room. As he got closer to the plane he phased inside of it to see Storm, Wolverine and Beast all staring at him. He then looked to the side to see Nick Fury flying the plane.

It didn't take long for the two groups to quickly meet in the hotel room. Both were hostile to each other but they weren't there to fight but capture Magento.

"How do you know about Magneto?" Beast asked as he looked around the room.

"He attacked us, he's looking for Wanda Maximoff. Why are you after him?" Tony replied.

"We've known him for a while now, he recently escaped from a Hydra prison cell. We don't know what he's going to do." Beast explained.

"How are you caught up in this Fury?" Tony asked.

"Magneto is one of the most dangerous men on the planet. He makes Loki look sane and as powerful as they come...He also wants to attack a nation where their major resource is metal." Fury explained.

"He also manipulates metal so you three would have been in the dirt in seconds." Logan interrupted and laughed, the Avengers weren't happy.

"Then we'll get him next time," Tony replied.

 **X**

The students of the Xavier institute were seen as some of the most gifted people in the world but to the students themselves they were cursed. This was true for David Haller, the son of Charles Xavier. He wasn't the most sociable teenager which was saying something in a school filled with people who were terrified of themselves. He was walking down the corridor, heading for the library. He couldn't concentrate, something was distracting him but he couldn't work out what it was.

 _Release me_

"Watch it, don't wanna touch me sugah." Rogue yelled as David bumped into her. He stepped back, a little dazed by what he just heard. He looked at the girl with the white stripe in her hair who had her eyebrow raised higher than the eiffel tower.

"Sorry Rogue."

"Y'all alright?" She asked as he leaned against the wall, his head felt like it was on fire.

"Yeah, just need to rest," David said as he returned back to his bedroom.

 _Release me, set me free and unleash me upon the world so that we can reclaim our position in the world._

"Who are you?" David screamed as he collapsed in front of his mirror, his head was burning and the walls were starting to move. He could barely see, it was like it was raining inside the room.

 _I am many David, you're barely even one...Let me out and I can make you whole. I can make her love you just let me out._

David screamed and looked into the mirror. His hair was now blonde and spiked whilst his eyes had turned green and he had adopted a scottish accent.

" _The time has come."_ He whispered to himself.

 **X**

The night sky of New Orleans always attracted a wide range of crowds. There were the party people who drank and danced the night away, the people who served the drinks and the people who hoped to steal wallets to pay for those drinks, it was a mess but for Remy Lebeau it was his home. He ran the nightclub Creole, a front for the Thieves Guild which he ran after his father's death.

He spent his evenings playing the piano whilst sipping bourbon, he had been dying of boredom ever since he hired a young runaway, Laura as his bouncer which he knew he was soon to regret. As he played his piano, he heard the door open but it was not the potential customer he was hoping for.

Laura got up and walked towards Erik and his two grandchildren. Remy raised his hand and Laura stopped, he then turned to the three and flashed them a devlish grin that occompanied his glowing red eyes.

"You know you can't have minors here mon ami?" Remy said as he took a sip of his drink. The twins struggled to understand the cajun but Erik just walked towards Remy and grabbed then glass straight out of his hand and finished the bourbon.

"Around these parts that's considered awfully rude." Remy said as he raised his hand and a waitress brought over another glass.

"Well, where I'm from it's considered acceptable to drink the drink of a man who forgets to offer." Erik said as he quickly grabbed the glass and took a swig before handing it to the angry cajun.

"Touche. What brings the Magneto here? Aren't you supposed to have been dead for thirty years." Remy asked as he reclaimed his glass. He remembered his father Jean-Luc telling him stories about his time with Erik Lensherr and his ironclad bladder.

"Well here I am...Now, back in the golden days I made a deal with your father. He'd provide me with guns and I'd pay him a handsome amount." Erik explained.

"And you want to revive that deal?" Remy asked, reviving his devilish grin.

"In a sense. Rumour has it, you can destroy an army with a playing card and in possession of a girl who can do just as much damage without the card." Erik asked.

"That's her." Remy said as he pointed to Laura, the young runaway he found on the streets and felt a sense of pity.

"Give me your wrist." Erik asked as he walked over to her. He showed her his, revealing the numbers on his. She looked at Remy who nodded and showed him hers. Like him, she had been tattooed but instead of numbers, it was 'X-23'.

"Welcome to the Brotherhood," Erik said smiling.


End file.
